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Detailed information for vg1119868109:

Variant ID: vg1119868109 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 19868109
Reference Allele: AAlternative Allele: G,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.70, A: 0.29, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


TGTATTTGCACAACACGCACAATTTAGTAGTTTTGAGAACATGCTCAAGATAAATGAGGGAGCCAATCTGATAAACACTTTACAACTCAACCTTAAATTT[A/G,T]
TTACTTATGTACTTAAAAAATACGTACAAATCAAAAGCGTAGATTGAGTCGTTAACGGCTAAAATTCAAACCGTGTTTAGCGAGAAAAAACATGCAACTT

Reverse complement sequence

AAGTTGCATGTTTTTTCTCGCTAAACACGGTTTGAATTTTAGCCGTTAACGACTCAATCTACGCTTTTGATTTGTACGTATTTTTTAAGTACATAAGTAA[T/C,A]
AAATTTAAGGTTGAGTTGTAAAGTGTTTATCAGATTGGCTCCCTCATTTATCTTGAGCATGTTCTCAAAACTACTAAATTGTGCGTGTTGTGCAAATACA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 35.50% 28.70% 24.02% 11.74% T: 0.08%
All Indica  2759 51.60% 9.50% 31.24% 7.68% NA
All Japonica  1512 8.20% 54.80% 14.55% 22.22% T: 0.26%
Aus  269 40.50% 48.30% 10.78% 0.37% NA
Indica I  595 26.90% 20.00% 39.33% 13.78% NA
Indica II  465 56.10% 3.70% 34.41% 5.81% NA
Indica III  913 68.20% 4.70% 23.33% 3.72% NA
Indica Intermediate  786 48.20% 10.60% 32.44% 8.78% NA
Temperate Japonica  767 5.90% 80.10% 6.26% 7.30% T: 0.52%
Tropical Japonica  504 12.50% 27.20% 22.82% 37.50% NA
Japonica Intermediate  241 6.60% 32.00% 23.65% 37.76% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 23.30% 43.30% 26.67% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1119868109 A -> T LOC_Os11g34000.1 upstream_gene_variant ; 4024.0bp to feature; MODIFIER silent_mutation Average:6.318; most accessible tissue: Callus, score: 11.361 N N N N
vg1119868109 A -> T LOC_Os11g33990.1 downstream_gene_variant ; 2214.0bp to feature; MODIFIER silent_mutation Average:6.318; most accessible tissue: Callus, score: 11.361 N N N N
vg1119868109 A -> T LOC_Os11g33970.1 intron_variant ; MODIFIER silent_mutation Average:6.318; most accessible tissue: Callus, score: 11.361 N N N N
vg1119868109 A -> DEL N N silent_mutation Average:6.318; most accessible tissue: Callus, score: 11.361 N N N N
vg1119868109 A -> G LOC_Os11g34000.1 upstream_gene_variant ; 4024.0bp to feature; MODIFIER silent_mutation Average:6.318; most accessible tissue: Callus, score: 11.361 N N N N
vg1119868109 A -> G LOC_Os11g33990.1 downstream_gene_variant ; 2214.0bp to feature; MODIFIER silent_mutation Average:6.318; most accessible tissue: Callus, score: 11.361 N N N N
vg1119868109 A -> G LOC_Os11g33970.1 intron_variant ; MODIFIER silent_mutation Average:6.318; most accessible tissue: Callus, score: 11.361 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1119868109 NA 1.37E-06 mr1179 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 1.79E-06 mr1285 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 8.88E-06 mr1502 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 3.40E-10 mr1549 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 5.06E-06 mr1596 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 2.44E-06 mr1729 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 1.14E-07 mr1746 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 7.74E-09 mr1757 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 8.34E-06 mr1788 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 5.47E-06 mr1871 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 3.10E-08 mr1364_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 9.37E-07 mr1570_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 4.10E-10 mr1746_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 4.93E-06 mr1757_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1119868109 NA 3.92E-08 mr1871_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251